schrodinger.livedesign.bbchem_endpoints module¶

Collection of functions intended as bbchem web endpoints.

schrodinger.livedesign.bbchem_endpoints.split_data_blocks(data: str, input_format: schrodinger.rdkit_extensions.Format, options: Optional[schrodinger.livedesign.registration.RegistrationOptions] = None)¶

Iterates across serialized formats, yielding a single data block at a time. Supports iterating across SD, Maestro, and FASTA files; other formats are returned as a single block. NOTE: if a FASTA mapping is set on the registration options, the FASTA is parsed as a single block.

Parameters

data – input text string
input_format – input format of the data
options – registration options

Returns

an iterator of data blocks

schrodinger.livedesign.bbchem_endpoints.to_registration_data(data: str, input_format: schrodinger.rdkit_extensions.Format, options: Optional[schrodinger.livedesign.registration.RegistrationOptions] = None) → Iterator[Union[schrodinger.livedesign.registration.RegistrationData, Exception]]¶: Generalizes small molecule and biologics registration processes, returning all data LiveDesign stores in it’s internal databases. This includes returning rdmol binaries directly as for each entity. Output includes properties from the input mol, computed properties, and potentially any child data of derived virtuals.

schrodinger.livedesign.bbchem_endpoints.to_format(mol_input: str, input_format: schrodinger.rdkit_extensions.Format, output_format: schrodinger.rdkit_extensions.Format, additional_properties: Optional[Dict] = None) → str¶

Main entrypoint for converting to a serialized text format.

Parameters

mol_input – serialized mol
input_format – input format of the mol string
output_format – desired format for output string
additional_properties – property data to include on serialization

Returns

converted text string

schrodinger.livedesign.bbchem_endpoints.to_image(mol_input: str, fallback_entity: Optional[schrodinger.livedesign.entity_type.EntityClass] = None, options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → bytes¶

Generates an image from a serialized input string

Parameters

mol_input – serialized mol
fallback_entity – entity class to use for a fallback image
options – image generation options

Returns

generated image SVG or PNG bytes

schrodinger.livedesign.bbchem_endpoints.to_fingerprint(mol_input: str, use: schrodinger.livedesign.search.FingerprintUse, substructure_options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None) → rdkit.DataStructs.cDataStructs.ExplicitBitVect¶

Generates a substructure or similarity fingerprint for a given mol.

Parameters

mol_input – serialized mol
use – type of fingerprint to generate
substructure_options – substructure matching options

schrodinger.livedesign.bbchem_endpoints.num_substructure_matches(*args, **kwargs) → int¶

Returns: number of substructure/subsequence matches

schrodinger.livedesign.bbchem_endpoints.has_substructure_match(*args, **kwargs) → bool¶

Returns: whether any substructure/subsequence match was found

schrodinger.livedesign.bbchem_endpoints.to_sequence_viewer_data(mol_binary_str: str, scheme: schrodinger.infra.util.AntibodyCDRScheme = AntibodyCDRScheme.Kabat) → Dict[str, Dict]¶

Returns: biologics sequence viewer data for the given mol

schrodinger.livedesign.bbchem_endpoints.generate_image(mol: rdkit.Chem.rdchem.Mol, alignment_mol: Optional[rdkit.Chem.rdchem.Mol] = None, substructure_options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None, highlight_mol: Optional[rdkit.Chem.rdchem.Mol] = None, draw_options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → bytes¶

Generates an image used in LiveDesign which may have a request for compound alignment, or substructure highlighting, or both.

Parameters

mol – compound to generate an image of
alignment_mol – molecule to align to prior to image generation
substructure_options – substructure matching options
highlight_mol – core to highlight in generated image
draw_options – image generation options

Returns

generated image as a string

schrodinger.livedesign.bbchem_endpoints.generate_sar_analysis_image(match_mol: rdkit.Chem.rdchem.Mol, scaffold_mol: rdkit.Chem.rdchem.Mol, substructure_options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None, draw_options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → bytes¶

Generates an image used in LiveDesign that is specifically from SAR analysis output, highlighting the core and all r-groups from the decomposition.

Parameters

match_mol – source molecule for R-group decomposition to highlight and generate image of
scaffold_mol – scaffold molecule on which to find R-groups
substructure_options – substructure matching options
draw_options – image generation options

Returns

generated image as a string

schrodinger.livedesign.bbchem_endpoints.pop_properties(mol: rdkit.Chem.rdchem.Mol) → dict¶

Parameters: mol – molecule to extract, then clear all properties from
Returns: map of all removed properties as strings

schrodinger.livedesign.bbchem_endpoints.set_properties(mol: rdkit.Chem.rdchem.Mol, new_props: dict)¶

Parameters

mol – molecule to clear, then set given properties on
new_props – map of properties to add onto the molecule

schrodinger.livedesign.bbchem_endpoints.split_fragments(mol: rdkit.Chem.rdchem.Mol)¶

Param: input molecule
Returns: iterable containing each fragment mol

schrodinger.livedesign.bbchem_endpoints.enumerate_stereoisomers(mol: rdkit.Chem.rdchem.Mol, max_stereoisomers: int = 512) → Iterator[rdkit.Chem.rdchem.Mol]¶

Generates stereoisomers from a specified SDF structure string.

Parameters

structure – structure from which to generate stereoisomers
max_stereoisomers – maximum number of stereoisomers to generate

Returns

generated stereoisomers

schrodinger.livedesign.bbchem_endpoints.rgroup_decompose(scaffold_mol: rdkit.Chem.rdchem.Mol, match_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None) → List[dict]¶

Decomposes a molecule into its core and R-groups given a scaffold

Parameters

scaffold_mol – scaffold molecule on which to find R-groups
match_mol – source molecule for R-group decomposition
stereospecific – whether to consider bond stereochemistry and atom chirality of scaffold

Returns

list of dicts of R-group matches

schrodinger.livedesign.bbchem_endpoints.get_rgroup_labels(scaffold_mol: rdkit.Chem.rdchem.Mol) → List[str]¶

Parameters: scaffold_mol – scaffold molecule
Returns: R-group labels present on the scaffold

schrodinger.livedesign.bbchem_endpoints.check_reaction(rxn_input: str) → schrodinger.livedesign.check_reaction.RxnCheckResult¶

schrodinger.livedesign.bbchem_endpoints.setup_reaction(rxn_input: str) → str¶

Tidy up and convert user sketched reactions into a format that can be used for reaction enumeration.

Parameters: rxn_input – a RXNBlock or RXNSMARTS describing the user’s reaction.
Returns: a SMARTS string describing the cleaned up reaction

schrodinger.livedesign.bbchem_endpoints.run_reaction(rxn_input: str, reactant_lists: List[List[str]], max_products: int = None, property_filters: dict = None) → Iterator[str]¶

Execute a reaction on one or more sets of reagents

Basically, each “reaction” can have one or more than reagents, and could be run on one or more sets of reagents.

Parameters

rxn_input – reaction definition in any supported format, such as RXN or reaction SMARTS.
reactant_lists – lists of reactants in any supported format, such as MOL or SMILES. Each list has to have the correct length, matching the number of reactant templates used by the reaction.
max_products – yield at most this many unique products. If not provided, all products are returned without limit or deduplication. (The canonical SMILES is used as the key.)
property_filters – dictionary with JSON data describing the property filters, with the schema expected by schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter.

Returns

generator of products in SDF format.

schrodinger.livedesign.bbchem_endpoints.get_PLDB_SMARTS(smiles: str) → Tuple[str, List]¶

Generates SMARTS from the given mol with a unique atom map number on each atom, which PLDB uses to indicate canonical atom indices. Also collects which of those indices are marked with the SKETCHER_SELECTED_PROP to return a list of the indices of all sketcher-selected atoms.

Parameters: mol – input SMILES
Returns: (PLDB compatible SMARTS pattern, list of selected atom indices)

schrodinger.livedesign.bbchem_endpoints.get_json_formatted_structure_hierarchy(mol_input: str, input_format: schrodinger.rdkit_extensions.Format) → str¶

Generates a JSON string representing the structure hierarchy of the molecule. This is used by LiveDesign to display the structure hierarchy viewer for the molecule and its components.

Note that this only process the first structure in the given string.

Parameters

mol_input – serialized mol
input_format – input format of the mol string

Returns

JSON string representing the structure hierarchy